Organic amendments (OAs) and soilborne biocontrol agents or beneficial microbes (BMs) have been extensively studied and applied worldwide in most agriculturally important plant species. However, poor integration of research and technical approaches has limited the development of effective disease management practices based on the combination of these two bio-based strategies. Insights into the importance of the plant-associated microbiome for crop productivity, which can be modified or modulated by introducing OAs and or BMs, are providing novel opportunities to achieve the goal of long-term disease control. This review discusses novel ways of functionally characterizing OAs and how they may be used to promote the effect of added biocontrol agents and or beneficial soil microbiota to support natural suppressiveness of plant pathogens.